BNFO 301
Introduction to Bioinformatics
Questionnaire on: Sequence-contrasts
(please press SUBMIT button when finished)
Spring 2008

I. Basic Information

A. Your name 

B. How far did you get in the notes? 

II. Detecting anomolous gene clusters...
A. Were you able to get the article by Samuel Karlin (2001)? 

B. The main focus of the article -- detection of pathogenic islands -- is not of great concern to us. Nonetheless, were you able to make sense out of the overall biology of the article? 

C. How comfortable are you with Figure 1, apart from the nuts and bolts of how the different quantities are calculated? 
Comments re Karlin (2001):

III. Calculating GC-fraction

A. How comfortable are you with the meaning of G+C fraction? Could you calculate it by hand if you had the time and patience? 

B. How comfortable are you calculating GC-FRACTION in BioBIKE? 

C. Do you appreciate the desirability of rounding off the fractions calculated by GC-FRACTION-OF? 

D. How comfortable are you with the MEANS of rounding off the fractions? 

E. How comfortable are you with the calculation of the statistics concerning the GC-fractions? 

F. How comfortable are you with using APPLY-FUNCTION to map a generalized function over a list of arguments? 

G. How comfortable are you with writing data to a file and finding that file afterwards? 

H. How comfortable are you with manipulating the data within Excel? 

I. Do you feel you understand why the distribution of GC-fractions change as the fragment size diminishes? 

D. Choose up to five study questions that you would most like discussed in class:

SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8  SQ9 
SQ10  SQ11  SQ12  SQ13  SQ14  SQ15  SQ16  SQ17 
 
Comments re
Calculation of GC-fractions:
IV. Meta-questions
A. Put here any miscellaneous comments, questions, suggestions, concerns you may have.
    For example, how are you doing with your sequence analysis? Is the world safe?
 

Thanks!

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